The report from the Infected Blood Inquiry said there had been ‘deliberate destruction' of relevant documents to conceal the scandal.
Chairman of the inquiry, Sir Brian Langstaff, said: ‘Standing back, and viewing the response of the NHS and of government overall, the answer to the question ‘was there a cover-up is that there has been.
‘Not in the sense of a handful of people plotting in an orchestrated way to mislead but in a way that was more subtle, more pervasive and more chilling in its implications.
‘In this way there has been a hiding of much of the truth.'
The report found there had been a deliberate decision to destroy Department of Health files which contained material dealing with delays in the introduction of screening blood donations for hepatitis C.
Sir Brian said: ‘Someone, for some reason, had chosen to have those documents destroyed.'
His ‘uncomfortable conclusion' was it was ‘more likely than not' the documents had been destroyed by a civil servant.
The report also said there was ‘the possibility' that missing health records could have been ‘filleted'.
Sir Brian added there was insufficient evidence that documents had been destroyed by health authorities ‘across the board'.
Over 30,000 people were infected with HIV and hepatitis C from 1970 to 1991 by contaminated blood products and transfusions with around 3,000 of them having since died.
Liberal Democrat leader Ed Davey said: ‘Our thoughts go to those whose lives have been torn apart by this disaster, and to the thousands of people who have died waiting for justice. Governments of all parties over decades owe them all a sincere apology.
‘This landmark report must finally lead to justice for all those impacted. It is critical that the Government compensates the victims and their families of this terrible scandal as quickly as possible.'